Flashcards in Lecture 27 - The 3D Structure Of Proteins Deck (15):
Polar amino acids
Non-polar/Hydrophobic amino acids (7)
Aromantic amino acids (3)
Charged amino acids (4)
Acidic alternatively negatively charged
Asp: Aspartic acid
Glu: Glutamic acid
Basic alternatively positively charged
Variable side chains indicate properties (5)
• Carboxyl groups COO- --> charged or acidic
• Amine groups NH3+ --> charged or basic
• 2^o Amine NH and Carbonyl C=O groups --> Polar
• Hydroxyl OH- --> Polar
• Hydrocarbon -->Non-polar Hydrophobic
Each repeating unit of the polypeptide is joined by a peptide bond.
Variable side chain, R is trans conformation.
Planar structure with rotational freedom within molecule found on alpha carbon.
Delocalised electrons of the N-CO make the bond rigid.
Glycines R group (H) allows greater flexibility of the peptide backbone.
Rotational freedom favours structural arrangements, alpha helices and beta sheets.
Energy minimisation (7)
• Each molecular structure has a specific energetic state.
• The minimisation of this energetic state (the free energy of a molecule “G”) determines the most favourable arrangement of the atoms (confirmation).
• The change in free energy upon folding is called ∆G.
• The free energy of any conformation is affected by the molecular environment.
o Aqueous or lipid membrane.
o Other proteins or molecules including salts and their ionic state.
o Changes in this environment can induce a further conformational change- for example a receptor binding a ligand.
Protein structure (4)
1. Primary structure
Covalent bonds forming polypeptide chain – i.e. order of amino acid residues joined by peptide bonds.
2. Secondary structure
Regular folded form, stabilised by hydrogen bonds – e.g. alpha helices, beta sheets and beta turns.
3. Tertiary structure
Overall 3D structure, stabilised by hydrogen bonds, hydrophobic, ionic and Van der Waal’s forces, and sometimes by intra-chain covalent (disulphide) bonds.
4. Quaternary structure
Organisation of polypeptides into assemblies, stabilised by non-covalent and Covalent bonds (as for Tertiary) and sometimes by inter-chain covalent (disulphide) bonds.
Bond folding - Non-Covalent bonds (5)
1/20th strength of covalent bonds.
Overall contribution is significant as non-covalent bonds are larger in number.
o Charge or electrostatic attractions
Falls off exponentially as distance increases, affected by electrostatic environment (aqueous environment).
o Hydrogen bonds
Occurs between polar groups like the carbonyl (C=O) and amide (NH) groups of the backbone.
o Van der Waals attractions – dipole
These weak forces occur between two atoms in non-covalent interactions. Determined by their fluctuating charge. Forces are induced by proximity of molecules.
o Hydrophobic interactions
(Water is a polar molecule) hydrophobic interactions minimise disruption of water network – i.e. the fourth weak force.
Bond folding - Covalent bonds (4)
o Disulphide bonds
Form in oxidative reaction.
The SH groups from each cysteine cross link.
Usually occurs in distant parts of the primary sequence but adjacent in the 3D structure.
Can form on the same (intra-chain) or different (inter-chain) polypeptide chains e.g. insulin.
Protein misfolding diseases (8)
• The function of the mis-folded protein is almost always lost or reduced.
• Misfolded proteins tend to self-associate and form aggregates
o Huntingtin Htt (Huntington’s).
o Amyloid-beta Ab (Alzheimer’s).
o Prion protein (PrPSc).
o alpha-synuclein (Parkinson’s disease).
o Serum amyloid A (AA amyloidosis).
o Islet amyloid polypeptide IAPP (Type 2 Diabetes)
• Other mis-folded proteins result in cellular processing that lead to their degradation.
o Cystic fibrosis
Misfolding can occur for several reasons (6)
Somatic mutations in the gene sequence leading to the production of a protein unable to adopt the native folding.
Errors in transcription or translation leading to the production of modified proteins unable to properly fold.
Failure of the folding machinery.
Mistakes of the post-translational modifications or in trafficking of proteins.
Structural modification produced by environmental changes.
Induction protein misfolding by seeding and cross-seeding by other proteins.
Protein misfolding - Alzheimer’s disease Amyloid hypothesis (9)
• In Alzheimer’s disease proteolytic cleavage of Amyloid Precursor Protein (APP) is observed.
• APP is a large transmembrane protein.
• APP has multiple functions but is involved in G-protein signalling.
• Proteolysis leads to cleavage of APP results in a @40 residue peptide -Amyloid (A).
• Misfolding of this protein results in a planar arrangement and polymerisation.
• This can form fibrils of mis-folded protein (amyloid fibrils).
• β-Amyloid (Aβ) fibres are formed from stacked beta sheets in which the side chains interdigitate.
• The aggregation of b-amyloid in the brains interfere with the workings of the synapse, particularly in the hippocampus.
• Higher order insoluble aggregates form, which contain much crossed -structure which become deposited in plaques, damaging the neuronal cells of brain.
Protein misfolding - Cystic fibrosis (5)
Most common mutation is deletion of Phenylalanine at residue 508 of the cystic fibrosis transmembrane conductance regulator (CFTR).
• DF508del leads to mis-folding of the protein whilst it is still in the ER.
• Recognised by the cellular machinery that identifies and processes misfolded protein.
• Results in ubiquitination, trafficking to the proteasome and degradation.
• 70% of Caucasian CF patients harbour this mutation.